Riboswitches are regulatory RNAs that recognize specific small molecules, usually key metabolites, and switch downstream gene expression on or off at either the transcriptional or translational level. The discovery of these short cis-acting RNA elements has drastically changed our understanding of genetic regulatory mechanisms. Riboswitches are especially prevalent in Gram-positive bacteria, exemplified by Bacillus subtilis as a model organism, but are also found to control essential genes in important pathogens such as Bacillus anthracis, Staphylococcus, Enterococcus, Streptococcus, Listeria, Clostridium, and Mycobacterium. This and other characteristics have attracted increasing attention to riboswitch-mediated regulation. The three distinct classes of S-adenosyl methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolution solutions to achieve specific SAM recognition. We recently determined the crystal structures of SAM riboswitches from two classes, the E. faecalis SMK box and the B. subtilis S box. These structures shed light into the how SAM is specifically recognized, but did not provide enough evidence to support the large SAM-dependent conformational changes observed in the previous genetic and biochemical studies. To fully understand their structure-functional relationship and conformational dynamics, we propose to: (1) Understand the ligand recognition mechanism in the SMK box riboswitch. (2) Characterize the ligand-free SMK conformation and search for eukaryotic riboswitches. (3) Carry out chemical probing experiments to reveal ligand-induced conformational dynamics in the SMK RNA